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The HIV Env Trimer Structure Unveiled

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Just how the human immunodeficiency virus type 1 (HIV-1) envelope trimer (a protein comprised of three subunits) assembles itself, then shifts its shape during infection has been difficult to define. But in two papers published in the October 31 issue of Science (“Cryo-EM structure of a fully glycosylated soluble cleaved HIV-1 envelope trimer” and “Crystal structure of a soluble cleaved HIV-1 envelope trimer”), collaborating scientists at The Scripps Research Institute (TSRI) and Weill Medical College of Cornell University have not only provided higher-resolution visuals of the Env trimer, but validated their findings using two different techniques. Other scientists on the team effort worked at Ragon Institute of MGH, MIT, and Harvard and the Academic Medical Center in Amsterdam, Netherlands. Knowledge of the protein’s structure, the scientists say, will potentially facilitate the design of a vaccine.

The HIV-1 envelope glycoprotein (Env) spike can act as a “molecular machine” that mediates virus entry into host cells, but is also the sole target for virus-neutralizing antibodies. The mature Env spike results from cleavage of a trimeric glycoprotein precursor, gp160, into three gp120 and three gp41 subunits. The resulting cage-like architecture of the protein, unique among characterized viral envelope proteins, restricts antibody access, reflecting requirements imposed by HIV-1 persistence in the host, scientists say. Further, the protein is highly unstable, complicating structural studies greatly.

To get around this problem, the Cornell/Scripps team engineered a version of the Env trimer (three-component structure) with the stability and other properties needed for atomic-resolution imaging, yet retains virtually all the structures found on native Env. These gp140 trimers, the team said, are not only highly stable and homogeneous, but also have a near- native antigenicity profile and a well-defined shape when viewed by negative-stain electron microscopy (EM) at intermediate resolution.

Using cryo-electron microscopy and X-ray crystallography the team was then able to look at the new Env trimer. The X-ray crystallography study was the first ever of an Env trimer, and both methods resolved the trimer structure to a finer level of detail than has been reported before.

Critical features of broadly neutralizing antibody (bnAb) epitopes have previously been revealed by x-ray structures of Fab complexes with the gp120 core, gp120 outer domain, gp41 peptides, scaffolded epitopes, or glycan arrays, the authors say. But, they note, these structures are based only on a sub-component of the Env spike and did not reveal the full complement of inter-subunit contacts and constraints. Low-resolution EM structures of the trimer provide an overall architecture but do not define the molecular details of bnAb epitopes needed to design an effective anti-HIV vaccine.

To comprehensively visualize the molecule’s molecular details, the scientists used cryo-electron microscopy to study soluble, cleaved, and stabilized recombinant trimers. Scripps’ Jean-Philippe Julien and colleagues allowed the Env trimer to bind a broadly neutralizing antibody, and then they crystallized the resulting complex at 4.7 Angstroms.

In a related experiment using the same trimer molecule but a different antibody, a group of scientists lead by Dimtry Lyumkis at Scripps performed cryo-electron microscopy.

The cryo-EM structure obtained by Lyumkis et al., and reported in the current published work agreed with the crystallographic structure presented by Julien’s group, providing previously unattainable insights into the trimer’s conformation prior to its fusion with a cell.

This work represents a major step forward in scientists’ understanding of the HIV entry mechanism. Because it presents a detailed picture of the Env trimer structure, it could help guide the design of structure-based vaccines.

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